Another new Fish Picker, version 4.0.6 is out:
http://home.wanadoo.nl/sfinx98/progs/picker_ma2.zip
Options to start Fish Picker minimized and to minimize it when launching the aquarium are added. The "Start/Stop" button now has a "hidden" option to make Fish Picker launch the aquarium when it starts. Just right-click the button.
memilm, could you try if the "Stop" button works for you now? If it still doesn't there should at least be an error message saying "Fish Picker could not close... "
And a similar question to riz, could you restore the settings that caused the failure with cycling the custom settings and try again?